Entering edit mode
5.1 years ago
zizigolu
★
4.3k
Hi,
I am trying to determine copy number in tumor and normal sample, so I calculated depth and so on by mosdepth and I finished with this table
https://www.dropbox.com/s/11jlie6kufibg4y/all_depth.txt?dl=0
> head(all_depth)
Chr Start Counts.100Tumor Counts.100Normal diff
1 1 0 0.00 0.00000 0.000000
2 1 10000 55.21 69.75838 -14.548375
3 1 20000 32.24 34.81226 -2.572259
4 1 30000 33.36 36.21775 -2.857753
5 1 40000 24.45 26.22632 -1.776319
6 1 50000 35.73 34.33420 1.395800
>
ggplot(all_depth[all_depth$Chr == "chr6",], aes(x=Start, y=diff, color=diff)) + geom_point() + scale_color_viridis("Depth", option = "plasma")
I was going to plot that like this picture from tutorial
But R gives me an empty plot, do you know why? I don't know where I am doing wrong I even tried for all chromosomes